BOL: Related items

A web-based tool for sequence alignment statistics and innovative visualization

BioStar — Thu, 04 Apr 2024 01:44:50 -0500

AlignStatPlot, a new R package and online tool that is well-documented and easy-to usefor MSA and post-MSA analysis. This tool performs both traditional and cutting-edge analy-ses on sequencing data and generates new visualisation methods for MSA results. Whencompared to currently available tools, AlignStatPlot provides a robust ability to handle andvisualise diversity data, while the online version will save time and encourage researchersto focus on explaining their findings. It is a simple tool that can be used in conjunction withpopulation genetics software (PDF) AlignStatPlot: An R package and online tool for robust sequence alignment statistics and innovative visualization of big data.

Address of the bookmark: https://bioinformatics.um6p.ma/AlignStatPlot/

Krona

Jit — Wed, 22 Mar 2017 04:47:35 -0500

Krona allows hierarchical data to be explored with zooming, multi-layered pie charts. Krona charts can be created using an Excel template or KronaTools, which includes support for several bioinformatics tools and raw data formats. The interactive charts are self-contained and can be viewed with any modern web browser (see Browser support).

Address of the bookmark: https://github.com/marbl/Krona/wiki

Mulan: MUltiple sequence Local AligNment and conservation visualization tool

Rahul Nayak — Thu, 20 Jul 2017 08:02:32 -0500

Mulan performs multiple (2 or more) sequence alignments with an efficient and rapid "full local" alignment strategy that ensures a recapitulation of evolutionary sequence rearrangements (such as inversions and reshuffling) in any of the species. It combines refine and tba tools to align either "draft" or "finished" quality sequences. Mulan provides a dynamic graphical interface to align and visualize conservation profiles for evolutionarily distant and closely related species.

Input formats, automated data upload from the UCSC Genome Browser, gene annotation, annotation of repetitive elements, and progress report were previously described in the zPicture instructions and we refer the users to these materials for more details. This introduction is mainly focused on some novel features unique to the Mulan.

Address of the bookmark: https://mulan.dcode.org/mulanInstructions.php

Graph Genome Suite

Jit — Fri, 28 Oct 2016 07:59:54 -0500

Seven Bridges is the biomedical data analysis company accelerating breakthroughs in genomics research for cancer, drug development and precision medicine. We build self-improving systems to analyze millions of genomes, including the Graph Genome Suite — the most advanced population genomics tools in the world.

Address of the bookmark: https://www.sbgenomics.com/graph/

Rectangle Graph for Repeat Resolution in Genome Assembly

Rahul Nayak — Thu, 28 Dec 2017 09:43:03 -0600

Ultimate tool for resolving repeats in genome assemblies.

Though the specific implementation of the idea of the rectangle graph approach is already included into the current SPAdes distribution, we're also releasing the Rectangle Graph Module (RGM) as the separate code which can be run independently of SPAdes. Although RGM differs from the current implementation of the rectangle graph approach in SPAdes, in the future we plan to integrate RGM in SPAdes. RGM can be run with other genome assemblers if they use the graph format as SPAdes files.

For more details see: Nikolay Vyahhi, Son K. Pham, Pavel Pevzner. From de Bruijn Graphs to Rectangle Graphs for Genome Assembly, Lecture Notes in Bioinformatics 7534 (2012), pp. 249-261.

Address of the bookmark: http://bioinf.spbau.ru/en/rectangles

PPanGGOLiN: Depicting microbial species diversity via a Partitioned PanGenome Graph Of Linked Neighbors

LEGE — Thu, 01 Feb 2024 00:24:32 -0600

PPanGGOLiN (Gautreau et al. 2020) is a software suite used to create and manipulate prokaryotic pangenomes from a set of either genomic DNA sequences or provided genome annotations. It is designed to scale up to tens of thousands of genomes. It has the specificity to partition the pangenome using a statistical approach rather than using fixed thresholds which gives it the ability to work with low-quality data such as Metagenomic Assembled Genomes (MAGs) or Single-cell Amplified Genomes (SAGs) thus taking advantage of large scale environmental studies and letting users study the pangenome of uncultivable species.

A complete documentation is available here.

Address of the bookmark: https://github.com/labgem/PPanGGOLiN

pggb: the pangenome graph builder

biogeek — Sun, 13 Sep 2020 20:54:20 -0500

This pangenome graph construction pipeline renders a collection of sequences into a pangenome graph (in the variation graph model). Its goal is to build a graph that is locally directed and acyclic while preserving large-scale variation. Maintaining local linearity is important for the interpretation, visualization, and reuse of pangenome variation graphs.

Address of the bookmark: https://github.com/pangenome/pggb

AlfaPang: alignment free algorithm for pangenome graph construction

BioStar — Thu, 28 Aug 2025 02:56:35 -0500

AlfaPang constructs variation graphs, leveraging its alignment-free and reference-free approach, based solely on intrinsic sequence properties. This design allows AlfaPang's runtime and memory usage to scale linearly with the size of input sequences, enabling it to handle significantly larger genome sets compared to other methods.

Address of the bookmark: https://github.com/AdamCicherski/AlfaPang

Recombination detection tool

Jit — Tue, 02 Feb 2016 10:11:14 -0600

A program to detect recombination hotspots using population genetic data.

More at https://github.com/auton1/LDhot

Address of the bookmark: https://github.com/auton1/LDhot

RASTtk : algorithm for building custom annotation pipelines and annotating batches of genomes

Abhi — Wed, 27 Apr 2016 11:07:59 -0500

The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offers a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.

More at http://www.nature.com/articles/srep08365

Address of the bookmark: http://rast.nmpdr.org/